The phrase "alignment containing" is correct and usable in written English.
It can be used in contexts where you are describing a specific type of alignment that includes certain elements or features.
Example: "The alignment containing the necessary parameters was successfully implemented in the system."
Alternatives: "alignment that includes" or "alignment featuring".
This resulted in an alignment containing 2366 sequences aligned across YidC helices TM2-TM6.
After removing poorly aligned columns we obtained an alignment containing 848 nucleotides that was used for the estimation of long-term begomovirus substitution rates.
Initially, we generated several variants of an alignment containing the entire set of compounds (Supporting Figure S1).
The alignment was modified manually using MacClade 3.08 [57] and exported in NEXUS format for further analysis with the final alignment containing 3261 sites.
Positive selection was further investigated using a sliding window approach, and adding the mRNA sequences of E. multilocularis to the alignment containing the distinct eg95 clones (Fig. 4b).
An initial structure alignment containing the CIDs from 1ITX, 1D2K, and 1LG1 was generated with the online CE-MC - multiple protein structure alignment program [69].
Since the single dataset analyses did not uncover conflicts between datasets except within V. dahliae, the five datasets were concatenated into one alignment containing 95 taxa and 3007 characters, and analyzed using Bayesian inference, parsimony, and maximum likelihood.
For each block, b in the alignment containing nb sequences and mb columns, the ith column of the block is assigned a score Cbi = 1 if all the residues in the column are aligned correctly, otherwise Cbi = 0.
3067 bp of the alignment containing the control region between tRNA-Pro and tRNA-Phe were not well aligned due to high sequence divergence and were therefore removed, resulting in an alignment of 16,352 bp for phylogenetic analyses.
For several other MIRNA arm-gene alignments, such as those containing miR862, miR447a and miR853, the miRNA-region of the alignment is similar to, or weaker than, the alignment containing flanking arm sequences (Figure 5).
Previous studies on HML2 have shown that transcripts may be promoted by the AATAAA motif [34] and that the putative TATA of HML4 is not conserved in an alignment containing five HML4:s from higher primates [55].
